That last point is why I led with the moral/allegorical interpretation of the passage.  Frankly, I don't fully understand why God would command the Israelites to kill all of the Canaanites, but I do understand that when I read it today, I can understand it as an admonition to aggressively root out all the things in my life that will draw me away from God.

Yet, we can't simply discard the literal meaning of the text, and those passages are definitely among the most difficult to understand literally, at least from a moral framework shaped by the incarnation, death, and resurrection of God.

God also allowed divorce in ancient Israel, but Jesus forbids it to Christians.  Is this a contradiction?  It sure can feel that way sometimes.  Is God "allowed" to command what he pleases?  Yes.

Now, this goes back to the ancient question: "Does God commands something because it is just, or is it just because he commands it?"  I tend towards the Medieval view of divine simplicity—that God is identical with all of his attributes.  So God and justice are the same thing.  Which suggests to me that if these passages of Scripture don't *appear* just, it must be because I am failing to grasp some underlying unity.

All this isn't much in the way of answers, but it's how I try to think about such things.